[English] 日本語
Yorodumi
- PDB-1k9m: Co-crystal structure of tylosin bound to the 50S ribosomal subuni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k9m
TitleCo-crystal structure of tylosin bound to the 50S ribosomal subunit of Haloarcula marismortui
Components
  • (RIBOSOMAL PROTEIN ...) x 28
  • 23S RRNA
  • 5S RRNA
KeywordsRIBOSOME / 50S subunit / tylosin / antibiotic
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / Helix Hairpins - #310 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / 50S ribosomal protein L10, archaea / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / : / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Ribosomal Protein L22; Chain A / Ribosomal protein L7Ae, archaea / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / N-terminal domain of TfIIb / Translation factors / Helix-hairpin-helix domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Single Sheet / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
: / : / TYLOSIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...: / : / TYLOSIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A.
CitationJournal: Mol.Cell / Year: 2002
Title: The structures of four macrolide antibiotics bound to the large ribosomal subunit.
Authors: Hansen, J.L. / Ippolito, J.A. / Ban, N. / Nissen, P. / Moore, P.B. / Steitz, T.A.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S RRNA
B: 5S RRNA
C: RIBOSOMAL PROTEIN L2
D: RIBOSOMAL PROTEIN L3
E: RIBOSOMAL PROTEIN L4
F: RIBOSOMAL PROTEIN L5
G: RIBOSOMAL PROTEIN L6
H: RIBOSOMAL PROTEIN L7AE
I: RIBOSOMAL PROTEIN L10
J: RIBOSOMAL PROTEIN L10E
K: RIBOSOMAL PROTEIN L13
L: RIBOSOMAL PROTEIN L14
M: RIBOSOMAL PROTEIN L15
N: RIBOSOMAL PROTEIN L15E
O: RIBOSOMAL PROTEIN L18
P: RIBOSOMAL PROTEIN L18E
Q: RIBOSOMAL PROTEIN L19E
R: RIBOSOMAL PROTEIN L21E
S: RIBOSOMAL PROTEIN L22
T: RIBOSOMAL PROTEIN L23
U: RIBOSOMAL PROTEIN L24
V: RIBOSOMAL PROTEIN L24E
W: RIBOSOMAL PROTEIN L29
X: RIBOSOMAL PROTEIN L30
Y: RIBOSOMAL PROTEIN L31E
Z: RIBOSOMAL PROTEIN L32E
1: RIBOSOMAL PROTEIN L37Ae
2: RIBOSOMAL PROTEIN L37E
3: RIBOSOMAL PROTEIN L39E
4: RIBOSOMAL PROTEIN L44E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,459,136265
Polymers1,451,91430
Non-polymers7,222235
Water141,9047877
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.902, 300.474, 575.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S RRNA


Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: RNA chain 5S RRNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779

+
RIBOSOMAL PROTEIN ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234

#3: Protein RIBOSOMAL PROTEIN L2 / 50S RIBOSOMAL PROTEIN L2P / HMAL2 / HL4


Mass: 25237.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#4: Protein RIBOSOMAL PROTEIN L3 / 50S RIBOSOMAL PROTEIN L3P / HMAL3 / HL1


Mass: 37265.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#5: Protein RIBOSOMAL PROTEIN L4 / 50S RIBOSOMAL PROTEIN L4E / HMAL4 / HL6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#6: Protein RIBOSOMAL PROTEIN L5 / 50S RIBOSOMAL PROTEIN L5P / HMAL5 / HL13


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#7: Protein RIBOSOMAL PROTEIN L6 / 50S RIBOSOMAL PROTEIN L6P / HMAL6 / HL10


Mass: 19830.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#8: Protein RIBOSOMAL PROTEIN L7AE / 50S RIBOSOMAL PROTEIN HS6


Mass: 12600.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#9: Protein RIBOSOMAL PROTEIN L10 / 50S RIBOSOMAL PROTEIN P0 / HMAL10 / L10E


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#10: Protein RIBOSOMAL PROTEIN L10E


Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS
#11: Protein RIBOSOMAL PROTEIN L13 / 50S RIBOSOMAL PROTEIN L13P / HMAL13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#12: Protein RIBOSOMAL PROTEIN L14 / 50S RIBOSOMAL PROTEIN L14P / HMAL14 / HL27


Mass: 14216.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#13: Protein RIBOSOMAL PROTEIN L15 / 50S RIBOSOMAL PROTEIN L15P / HMAL15 / HL9


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#14: Protein RIBOSOMAL PROTEIN L15E


Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS
#15: Protein RIBOSOMAL PROTEIN L18 / 50S RIBOSOMAL PROTEIN L18P / HMAL18 / HL12


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#16: Protein RIBOSOMAL PROTEIN L18E / 50S RIBOSOMAL PROTEIN L18E / HL29 / L19


Mass: 12307.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#17: Protein RIBOSOMAL PROTEIN L19E / 50S RIBOSOMAL PROTEIN L19E / HMAL19 / HL24


Mass: 16631.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#18: Protein RIBOSOMAL PROTEIN L21E / 50S RIBOSOMAL PROTEIN L21E / HL31


Mass: 10436.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#19: Protein RIBOSOMAL PROTEIN L22 / 50S RIBOSOMAL PROTEIN L22P / HMAL22 / HL23


Mass: 16835.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#20: Protein RIBOSOMAL PROTEIN L23 / 50S RIBOSOMAL PROTEIN L23P / HMAL23 / HL25 / L21


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#21: Protein RIBOSOMAL PROTEIN L24 / 50S RIBOSOMAL PROTEIN L24P / HMAL24 / HL16 / HL15


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#22: Protein RIBOSOMAL PROTEIN L24E / 50S RIBOSOMAL PROTEIN L24E / HL21/HL22


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#23: Protein RIBOSOMAL PROTEIN L29 / 50S RIBOSOMAL PROTEIN L29P / HMAL29 / HL33


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#24: Protein RIBOSOMAL PROTEIN L30 / 50S RIBOSOMAL PROTEIN L30P / HMAL30 / HL20 / HL16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#25: Protein RIBOSOMAL PROTEIN L31E / 50S RIBOSOMAL PROTEIN L31E / L34 / HL30


Mass: 10253.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#26: Protein RIBOSOMAL PROTEIN L32E / 50S RIBOSOMAL PROTEIN L32E / HL5


Mass: 26324.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#27: Protein RIBOSOMAL PROTEIN L37Ae


Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS
#28: Protein RIBOSOMAL PROTEIN L37E / 50S RIBOSOMAL PROTEIN L37E / L35E


Mass: 6199.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#29: Protein/peptide RIBOSOMAL PROTEIN L39E / 50S RIBOSOMAL PROTEINS L39E / HL39E / HL46E


Mass: 5844.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#30: Protein RIBOSOMAL PROTEIN L44E / 50S RIBOSOMAL PROTEIN L44E / LA / HLA


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411

-
Non-polymers , 7 types, 8112 molecules

#31: Chemical ChemComp-TYK / TYLOSIN


Mass: 916.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H77NO17
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 119 / Source method: obtained synthetically / Formula: Mg
#33: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: Na
#34: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#35: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#36: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#37: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7877 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.8
Details: PEG 6K, KCl, Na-acetate, NH4Cl, MgCl2, pH 5.8, VAPOR DIFFUSION, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NaOAC11
4NH4Cl11
5MgCl211
Crystal grow
*PLUS
pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.2 M1reservoirKCl
20.5 M1reservoirNH4Cl
3100 mMKacetate1reservoir
430 mM1reservoirMgCl2
57 %PEG60001reservoir
615 mMTris1reservoir
715 mMMES1reservoir
81 mM1reservoirCdCl2pH7.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 27, 2000
RadiationMonochromator: Si-111, Si-220 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 366365 / Num. obs: 366365 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 12.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / Num. unique all: 34695 / Rsym value: 0.709 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 92.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.15
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 79.5 % / Rmerge(I) obs: 0.67

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JJ2

1jj2


Resolution: 3→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 435172.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: RNA modified from Brunger and Bergman Tylosin parameters constructed from xplo2d based on CSD small molecule structures PRTYLD, LANKVL10, and NAVTAF, and standard stereochemical parameters
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3303 1 %RANDOM same as 1JJ2
Rwork0.219 ---
all0.219 359798 --
obs0.219 337448 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.4751 Å2 / ksol: 0.300425 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1-12.15 Å20 Å20 Å2
2---5.96 Å20 Å2
3----6.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28801 61617 298 7877 98593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.242
X-RAY DIFFRACTIONc_scangle_it1.992.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 290 1 %
Rwork0.334 28404 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1RNA_JEFF.PARAM5RNA_JEFF.TOP5
X-RAY DIFFRACTION2PROTEIN_JEFF.PARAM3PROTEIN_TYM.TOP3
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION5TYLF_JEFF_PRT_CIN_3.PARTYLF_JEFF_PRT_CIN_3.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more